MolNFT v1 · #186773 · protein
X-ray crystal structure of oxa-24/40 V130D in complex with imipenem
7RP9 · Beta-lactamase: “X-ray crystal structure of oxa-24/40 V130D in complex with imipenem”. X-ray diffraction, 4 ligands (ID1, HIW, BCT), 2 pockets (best druggability 0.41). MolNFT v1 #186773 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7RP9
- Type
- protein
- Length
- 244 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-lactamase
- EC
- 3.5.2.6
- UniProt
- Q8RLA6
- Ligands
- ID1, HIW, BCT, SO4
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-lactamase (EC 3.5.2.6) | protein | 244 | 40% helix, 21% strand | Q8RLA6 |
Ligands and binding sites
- ID1 · Imipenem · ligand · chains A
- HIW · (2R,4S)-2-[(1S,2R)-1-carboxy-2-hydroxypropyl]-4-[(2-{[(Z)-iminomethyl]amino}ethyl)sulfanyl]-3,4-dihydro-2H-pyrrole-5-carboxylic acid · ligand · chains A
- BCT · Bicarbonate ion · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.41 | 0.76 | 17 | ID1, HIW |
| 2 | 51 | 0.27 | 0.74 | 16 | empty |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7RP9 · X-ray crystal structure of OXA-24/40 V130D in complex with imipenem · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8RLA6
- Elsewhere: RCSB PDB 7RP9 · PDBe 7RP9 · UniProt Q8RLA6
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